The optical projection tomography microscope (OPTM) is an optical microscope that acquires focus-invariant images from multiple views of single cells. Although the depth of field of the objective is short, it can be extended by scanning the objective's focal plane. This extended depth of field image is similar to a projection in conventional X-ray CT. Samples flow through a microcapillary tube filled with optical gel. Optical distortion is minimized by matching refractive index of optical gel and tube. Multiple projection images are taken by rotating the microcapillary tube with sub-micron mechanical precision. After these pseudoprojection images are further aligned, computed tomography methods are then applied to the images to create a 3D reconstruction with isometric resolution of 0.35 microns. Three-dimensional reconstructed images of fluorescent microspheres and cells are shown.